Question: Unable To Go Through Biopython'S Motif Tutorial - Ioerror
1
gravatar for Olivier
6.9 years ago by
Olivier440
Olivier440 wrote:

Hello

I'm trying the Sequence motif analysis tutorial in the Biopython cookbook and it's not working. Can someone help? Here's how it is:

from Bio import Motif
arnt = Motif.read(open("Arnt.sites"), "jaspar-sites")
Traceback (most recent call last):
  File "<pyshell#1>", line 1, in <module>
    arnt = Motif.read(open("Arnt.sites"), "jaspar-sites")
IOError: [Errno 2] No such file or directory: 'Arnt.sites'
motif biopython • 1.8k views
ADD COMMENTlink modified 6.9 years ago by Leonor Palmeira3.7k • written 6.9 years ago by Olivier440
2

as it says: the file 'Arnt.sites' doesn't exist in your current working directory.

ADD REPLYlink written 6.9 years ago by Pierre Lindenbaum120k

You're right Pierre. But its location is not mentioned in the tutorial. Do you have an idea what "Arnt.sites" and "jaspar-sites" refer to? It's about JASPAR-formatted motifs but I don't know how to carry on.

ADD REPLYlink written 6.9 years ago by Olivier440
5
gravatar for Leonor Palmeira
6.9 years ago by
Leonor Palmeira3.7k
Liège, Belgium
Leonor Palmeira3.7k wrote:

These Arnt.sites and SRF.pfm from the BioPython manual are from the JASPAR database. Somewhere in here: http://jaspar.genereg.net/html/DOWNLOAD/

These are just example files to fill the manual, you should make your own in case you're doing your own analysis.

ADD COMMENTlink written 6.9 years ago by Leonor Palmeira3.7k
1
gravatar for Istvan Albert
6.9 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

add the Arnt.sites file to your work directory

ADD COMMENTlink written 6.9 years ago by Istvan Albert ♦♦ 80k

Could you please tell me where I can get this file? I can't really find it on the JASPAR database... unless it's something like this 'MA0001.1.sites'? Thanks

ADD REPLYlink written 6.9 years ago by Olivier440

You should definitely try those.

ADD REPLYlink written 6.9 years ago by Leonor Palmeira3.7k
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